Abstract

The protein family (Pfam) PF04536 is a broadly conserved domain family of unknown function (DUF477), with more than 1,350 members in prokaryotic and eukaryotic proteins. High-quality NMR structures of the N-terminal domain comprising residues 41–180 of the 684-residue protein CG2496 from Corynebacterium glutamicum and the N-terminal domain comprising residues 35–182 of the 435-residue protein PG0361 from Porphyromonas gingivalis both exhibit an α/β fold comprised of a four-stranded β-sheet, three α-helices packed against one side of the sheet, and a fourth α-helix attached to the other side. In spite of low sequence similarity (18%) assessed by structure-based sequence alignment, the two structures are globally quite similar. However, moderate structural differences are observed for the relative orientation of two of the four helices. Comparison with known protein structures reveals that the α/β architecture of CG2496(41–180) and PG0361(35–182) has previously not been characterized. Moreover, calculation of surface charge potential and identification of surface clefts indicate that the two domains very likely have different functions.

Keywords

CG2496 PG0361 CgR26A PgR37A PF04536 DUF477 Structural genomics

Abbreviations

C-Ala domain

C-terminal domain of alanyl-tRNA synthetase

DSS

4,4-dimethyl-4-silapentane-1-sulfonate sodium salt

DTT

Dithiothreitol

MES

2-(N-morpholino)ethanesulfonic acid

NESG

Northeast structural genomics consortium

NOE

Nuclear overhauser effect

PDB

Protein Data Bank

RMSD

Root mean square deviation

Electronic supplementary material

The online version of this article (doi:10.1007/s10969-011-9122-2) contains supplementary material, which is available to authorized users.